TB-Profiler result

Run: ERR4816437

Summary

Run ID: ERR4816437

Sample name:

Date: 01-04-2023 14:25:50

Number of reads: 1353032

Percentage reads mapped: 97.93

Strain: lineage3

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.31 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.33 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779004 c.19delG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801024 c.216C>G synonymous_variant 0.88
Rv1258c 1407060 p.Trp94* stop_gained 1.0
embR 1416199 c.1149G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.22
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.67
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.4
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.71
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.57
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.57
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.86
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.8
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.55
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.36
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.55
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.5
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.9
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.4
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.8
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.83
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.8
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.83
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.5
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.36
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.5
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.43
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.33
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.43
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.4
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.85
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.85
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.85
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.92
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.92
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.92
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.94
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.95
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.88
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.87
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.86
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.86
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.86
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.75
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.75
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.69
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.75
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.71
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.25
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.3
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.3
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.3
rrs 1473291 n.1446G>C non_coding_transcript_exon_variant 0.3
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.3
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.3
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.3
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.3
rrl 1473384 n.-274A>G upstream_gene_variant 0.22
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.75
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 1.0
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.6
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.6
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.4
rrl 1475758 n.2101_2102dupAC non_coding_transcript_exon_variant 1.0
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 1.0
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 1.0
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.6
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 1.0
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 1.0
rrl 1475769 n.2112_2113dupTG non_coding_transcript_exon_variant 1.0
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.6
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.4
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.2
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.27
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519134 c.1020G>A synonymous_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067234 p.Gly238Ser missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448393 c.-111G>A upstream_gene_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245964 p.Val911Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0